Generated summary
PXD022678 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 735,560 PSMs, 83,172 peptidoforms and 5,887 protein groups, and the repository holds 47,742 PTM sites for it. 4 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Open findings
Recorded against this dataset: 0 errors, 4 warnings and 2 for information
count_mismatch warning
The bundle holds 735560 where the producer reported 735666 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 735560 where the producer reported 735666 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
occupancy_not_stored warning
Of 120248 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7246 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
Of 120248 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7246 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
unplaced_ptm_sites warning
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 3284 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 3284 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 4 identifier(s), 13 row(s) dropped, e.g. PXD022678:A0A0J9YU00;A0A0J9YU01;A0AAG1GJS6;A0AAG1GNH3;A0AB53C405;D3YUJ6;J3QK78;J3QPH3 written 8 times; quant_values: 36 identifier(s), 117 row(s) dropped, e.g. PXD022678:Seq46617_QE3:label_free:protein_group:PXD022678:A0A0J9YU00;A0A0J9YU01;A0AAG1GJS6;A0AAG1GNH3;A0AB53C405;D3YUJ6;J3QK78;J3QPH3:QuantProject:DEF-PROT-SPC written 8 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 4 identifier(s), 13 row(s) dropped, e.g. PXD022678:A0A0J9YU00;A0A0J9YU01;A0AAG1GJS6;A0AAG1GNH3;A0AB53C405;D3YUJ6;J3QK78;J3QPH3 written 8 times; quant_values: 36 identifier(s), 117 row(s) dropped, e.g. PXD022678:Seq46617_QE3:label_free:protein_group:PXD022678:A0A0J9YU00;A0A0J9YU01;A0AAG1GJS6;A0AAG1GNH3;A0AB53C405;D3YUJ6;J3QK78;J3QPH3:QuantProject:DEF-PROT-SPC written 8 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
75 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
75 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
What was found
| PSMs at 1% FDR | 735,560 |
| Peptidoforms at 1% FDR | 83,172 |
| Protein groups at 1% FDR | 5,887 |
| PTM sites | 47,742 |
| Quantitative values | 488,471 |
| PSMs, all (including decoys and sub-threshold) | 1,105,709 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 95.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
How it was measured
- Organism searched
- Mus musculus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- none
- Instrument vendor
- not recorded
- Runs / samples
- 9 / 9
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 089bcc7b11dc
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 15,173 |
| Oxidation on M | UNIMOD:35 | 5,436 |
| Deamidation on N | UNIMOD:7 | 4,512 |
| Carbamyl on K | UNIMOD:5 | 3,691 |
| Carbamyl on X | UNIMOD:5 | 3,619 |
| Deamidation on Q | UNIMOD:7 | 3,336 |
| Hydroxylation on P | UNIMOD:35 | 856 |
| Citrullination on R | UNIMOD:7 | 755 |
| Ammonia loss on N | UNIMOD:385 | 647 |
| Fe[III] on E | UNIMOD:1870 | 528 |
| Ammonia loss on C | UNIMOD:385 | 503 |
| Fe[III] on D | UNIMOD:1870 | 435 |
| Sodium on E | UNIMOD:30 | 431 |
| Acetylation on K | UNIMOD:1 | 364 |
| Sodium on D | UNIMOD:30 | 361 |
| Magnesium on E | UNIMOD:956 | 347 |
| N-acetylalanine on A | UNIMOD:1 | 341 |
| Carbamyl on M | UNIMOD:5 | 332 |
| Acetylation on X | UNIMOD:1 | 288 |
| Methylation on K | UNIMOD:34 | 286 |
| Calcium on E | UNIMOD:951 | 274 |
| Hydroxylation on N | UNIMOD:35 | 266 |
| Magnesium on D | UNIMOD:956 | 261 |
| Phosphoserine on S | UNIMOD:21 | 258 |
| N6-acetyllysine on K | UNIMOD:1 | 242 |
| Hydroxylation on K | UNIMOD:35 | 225 |
| Calcium on D | UNIMOD:951 | 224 |
| Fe[II] on D | UNIMOD:952 | 223 |
| Fe[II] on E | UNIMOD:952 | 217 |
| Carboxylation on K | UNIMOD:299 | 192 |
| N-acetylmethionine on M | UNIMOD:1 | 192 |
| Carboxylation on E | UNIMOD:299 | 146 |
| N-acetylserine on S | UNIMOD:1 | 145 |
| Carbamyl on R | UNIMOD:5 | 125 |
| Dimethylation on K | UNIMOD:36 | 124 |
| Phosphorylation on S | UNIMOD:21 | 111 |
| Methylation on R | UNIMOD:34 | 108 |
| Trimethylation on K | UNIMOD:37 | 108 |
| Potassium on D | UNIMOD:530 | 106 |
| Potassium on E | UNIMOD:530 | 106 |
| Carboxylation on D | UNIMOD:299 | 94 |
| Water Loss on E | UNIMOD:27 | 85 |
| Dimethylation on R | UNIMOD:36 | 75 |
| Phosphorylation on T | UNIMOD:21 | 66 |
| Nitrosylation on Y | UNIMOD:354 | 58 |
| Formylation on K | UNIMOD:122 | 55 |
| Carbamyl on C | UNIMOD:5 | 52 |
| Phosphothreonine on T | UNIMOD:21 | 50 |
| HexNAc on T | UNIMOD:43 | 47 |
| HexNAc on S | UNIMOD:43 | 46 |
| Malonylation on K | UNIMOD:747 | 45 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 44 |
| Omega-N-methylarginine on R | UNIMOD:34 | 43 |
| N6-methyllysine on K | UNIMOD:34 | 42 |
| 4-hydroxyproline on P | UNIMOD:35 | 35 |
| Glutarylation on K | UNIMOD:1848 | 31 |
| N-acetylthreonine on T | UNIMOD:1 | 31 |
| Succinylation on K | UNIMOD:64 | 31 |
| Hydroxybutyrylation on K | — | 29 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 28 |
| Butyrylation on K | UNIMOD:1289 | 24 |
| Deamidated asparagine on N | UNIMOD:7 | 23 |
| N6-succinyllysine on K | — | 22 |
| Nitrosylation on C | UNIMOD:275 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Crotonylation on K | UNIMOD:1363 | 18 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 15 |
| Phosphorylation on Y | UNIMOD:21 | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| Sulfonation on Y | UNIMOD:40 | 14 |
| N6-glutaryllysine on K | — | 13 |
| Cu[I] on D | UNIMOD:531 | 10 |
| Cu[I] on E | UNIMOD:531 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N6-crotonyllysine on K | — | 7 |
| Pros-methylhistidine on H | UNIMOD:34 | 7 |
| Pyridoxal phosphate on K | UNIMOD:46 | 7 |
| Zinc on D | UNIMOD:954 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| N-acetylcysteine on C | UNIMOD:1 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| ADP-ribosylation on S | UNIMOD:213 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 4 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Hypusine on K | UNIMOD:379 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-methacryllysine on K | — | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N,N-dimethylproline on P | UNIMOD:529 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Zinc on E | UNIMOD:954 | 1 |
Every modification with a site on a target protein, most frequent first. A dash in the UNIMOD
column means the modification has no UNIMOD term in the registry that searched it, not that it is
unknown. One chemistry can appear under two names (UniProt's and MetaMorpheus's); the catalog's
ptm_sites_by_chemistry view merges them.
Data
The Parquet files for this dataset are not published yet.
- Bundle
e55d0cc1f3965d5c, written 2026-10-29T10:00:56+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group